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Feat: Use MorphIO by default and fallback to internal loader in case of failure #71

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Feat: Use MorphIO by default and fallback to internal loader in case of failure #71

Feat: Use MorphIO by default and fallbacks to internal loader in case…
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GitHub Actions / JUnit Test Report failed Sep 28, 2023 in 0s

92 tests run, 88 passed, 0 skipped, 4 failed.

Annotations

Check failure on line 174 in .tox/docs/lib/python3.9/site-packages/numpy/lib/tests/test_io.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_io.test_upper_case[True] 

ValueError: The file extension must be in ['asc', 'h5', 'swc']
Raw output 
DATA_PATH = '/home/runner/work/TMD/TMD/tests/data', use_morphio = True

    @pytest.mark.parametrize("use_morphio", [True, False])
    def test_upper_case(DATA_PATH, use_morphio):
        """Read files with upper-case extensions."""
        path = Path(DATA_PATH) / "upper_case_names"
        if use_morphio:
            files = path
        else:
            files = [i for i in path.iterdir() if i.suffix.lower() != ".asc"]
>       io.load_population(files, use_morphio=use_morphio)

tests/test_io.py:174: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tmd/io/io.py:252: in load_population
    pop.append_neuron(load_neuron(filename, user_tree_types=user_tree_types))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

input_file = '/home/runner/work/TMD/TMD/tests/data/upper_case_names/Sample2.SwC'
user_tree_types = None

    def load_neuron(
        input_file, user_tree_types=None, *, line_delimiter="\n", soma_type=None, remove_duplicates=True
    ):
        """I/O method to load an 'asc', 'h5' or 'swc' file into a Neuron object.
    
        Args:
            input_file (Union[str, morphio.Morphology]):
                Filepath or morphio object
    
        Returns:
            neuron (Neuron): tmd Neuron object
    
        """
        ext = os.path.splitext(input_file)[-1][1:]
        if ext not in ("h5", "swc", "asc"):
>           raise ValueError("The file extension must be in ['asc', 'h5', 'swc']")
E           ValueError: The file extension must be in ['asc', 'h5', 'swc']

tmd/io/io.py:196: ValueError

Check failure on line 174 in .tox/docs/lib/python3.9/site-packages/numpy/lib/tests/test_io.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_io.test_upper_case[False] 

ValueError: The file extension must be in ['asc', 'h5', 'swc']
Raw output 
DATA_PATH = '/home/runner/work/TMD/TMD/tests/data', use_morphio = False

    @pytest.mark.parametrize("use_morphio", [True, False])
    def test_upper_case(DATA_PATH, use_morphio):
        """Read files with upper-case extensions."""
        path = Path(DATA_PATH) / "upper_case_names"
        if use_morphio:
            files = path
        else:
            files = [i for i in path.iterdir() if i.suffix.lower() != ".asc"]
>       io.load_population(files, use_morphio=use_morphio)

tests/test_io.py:174: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tmd/io/io.py:252: in load_population
    pop.append_neuron(load_neuron(filename, user_tree_types=user_tree_types))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

input_file = PosixPath('/home/runner/work/TMD/TMD/tests/data/upper_case_names/Sample2.SwC')
user_tree_types = None

    def load_neuron(
        input_file, user_tree_types=None, *, line_delimiter="\n", soma_type=None, remove_duplicates=True
    ):
        """I/O method to load an 'asc', 'h5' or 'swc' file into a Neuron object.
    
        Args:
            input_file (Union[str, morphio.Morphology]):
                Filepath or morphio object
    
        Returns:
            neuron (Neuron): tmd Neuron object
    
        """
        ext = os.path.splitext(input_file)[-1][1:]
        if ext not in ("h5", "swc", "asc"):
>           raise ValueError("The file extension must be in ['asc', 'h5', 'swc']")
E           ValueError: The file extension must be in ['asc', 'h5', 'swc']

tmd/io/io.py:196: ValueError

Check failure on line 169 in tests/test_neuron_conversion.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_neuron_conversion.test_neuron_building_consistency__h5 

AttributeError: type object 'morphio._morphio.Option' has no attribute 'allow_root_bifurcations'
Raw output 
def test_neuron_building_consistency__h5():
        # noqa: D103 ; pylint: disable=missing-function-docstring
        path = f"{DATA_PATH}/valid/C010398B-P2.h5"
    
        neuron1 = load_neuron(path)
>       neuron2 = _load_neuron_morphio(path)

tests/test_neuron_conversion.py:169: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

path_or_obj = '/home/runner/work/TMD/TMD/tests/data/valid/C010398B-P2.h5'
user_tree_types = None

    def _load_neuron_morphio(path_or_obj, user_tree_types=None):
        """Create Neuron object from morphio object or from path loaded via morphio.
    
        Supported file formats: h5, swc, asc.
    
        Args:
            path_or_obj (Union[str, morphio.Morphology]):
                Filepath or morphio object
    
        Returns:
            neuron (Neuron): tmd Neuron object
        """
        tree_types = redefine_types(user_tree_types)
    
        if isinstance(path_or_obj, (str, Path)):
            obj = Morphology(
                path_or_obj,
>               Option.allow_root_bifurcations
                | Option.allow_soma_bifurcations
                | Option.allow_custom_root_id
                | Option.allow_multiple_somata,
            )
E           AttributeError: type object 'morphio._morphio.Option' has no attribute 'allow_root_bifurcations'

tmd/io/io.py:167: AttributeError

Check failure on line 183 in tests/test_neuron_conversion.py

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_neuron_conversion.test_neuron_building_consistency__swc 

AttributeError: type object 'morphio._morphio.Option' has no attribute 'allow_root_bifurcations'
Raw output 
def test_neuron_building_consistency__swc():
        # noqa: D103 ; pylint: disable=missing-function-docstring
        path = f"{DATA_PATH}/valid/C010398B-P2.CNG.swc"
    
        neuron1 = load_neuron(path)
>       neuron2 = _load_neuron_morphio(path)

tests/test_neuron_conversion.py:183: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

path_or_obj = '/home/runner/work/TMD/TMD/tests/data/valid/C010398B-P2.CNG.swc'
user_tree_types = None

    def _load_neuron_morphio(path_or_obj, user_tree_types=None):
        """Create Neuron object from morphio object or from path loaded via morphio.
    
        Supported file formats: h5, swc, asc.
    
        Args:
            path_or_obj (Union[str, morphio.Morphology]):
                Filepath or morphio object
    
        Returns:
            neuron (Neuron): tmd Neuron object
        """
        tree_types = redefine_types(user_tree_types)
    
        if isinstance(path_or_obj, (str, Path)):
            obj = Morphology(
                path_or_obj,
>               Option.allow_root_bifurcations
                | Option.allow_soma_bifurcations
                | Option.allow_custom_root_id
                | Option.allow_multiple_somata,
            )
E           AttributeError: type object 'morphio._morphio.Option' has no attribute 'allow_root_bifurcations'

tmd/io/io.py:167: AttributeError
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